Document 6509641

How to generate new tools and methods for
improving algal bioresources and the
domestication of seaweed species?
.
Final conference:
European Seaweed industry – current status and future perspectives
2012 DONOSTIA/SAN SEBASTIAN
Philippe POTIN and Idealg WP leaders
Nori farming in Japan
1921
Nori farming in Japan
1990
A reality in western countries
Chondrus crispus flowering (NS,
(NS Canada,
Canada ASP)
Hana-Tsunomata™ when
translated from Japanese
means "Flower
Chondrus". Other
common references to
Hana-Tsunomata™ sea
vegetables include Hananori™ ("Flower
seaweed"), Cultivated
Chondrus Kaede-nori
Chondrus,
Kaede nori
("Maple seaweed") and
Hana-sakura-sou
("Cherry blossom sea
plant").
2011--2010
2011
Seaweed biotechnology and bioresources
A national 1010-year large integrative project to merge
algal genomics with mariculture, biotechnology and chemistry.
chemistry.
1: Control of algal life cycles
Dr Kathleen Drew-Baker
1: Control of algal life cycles
L i i digitata
Laminaria
di it t life cycle and farming lif
l
df
i
2: Domestication
Decrease in branching and increase in seed size
were also selected for during
g corn domestication
Image credit Nicolle Rager Fuller,
National Science Foundation
2: Domestication
An example of a domesticated brown l f d
i
db
seaweed : Undaria pinnatifida
p
f
3. Towards genetic breeding
Advances iin genetic
Ad
ti ttechnologies
h l i should
h ld
contribute to improved seaweeds
•Marker assisted selection
•Genome-wide association studies
•Recombinant DNA technology
and transgenic plants , except in
closed systems
Photo credit: IRRI
3. Towards genetic breeding
M k assisted
Marker
i t d selection
l ti (MAS)
Phenotype: physical
expression of traits
Genotype: sequence of all the
genes in a genome
Photo credit LemnaTec; Anderson, L.K., Lai, A., Stack, S.M., Rizzon, C. and Gaut, B.S. (2006). Uneven
distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Research. 16: 115-122.
3. Towards genetic breeding
M k assisted
Marker
i t d selection
l ti (MAS)
Selecting for DNA
markers is faster than
selecting for
phenotype
Phenotype: physical
expression of traits
Genotype: sequence of all the
genes in a genome
Photo credit LemnaTec; Anderson, L.K., Lai, A., Stack, S.M., Rizzon, C. and Gaut, B.S. (2006). Uneven
distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Research. 16: 115-122.
Microsatellite markers to estimate genetic
diversity in L. digitata
Population 1
Low g
genetic diversity
y
Population 2
Forte diversité g
génétique
q
Each line corresponds
p
to an
individual:
189
189
187
187
24 individuals were studied in
population 1
e
185
183
185
183
They are all sharing the same
genotype
Th diversity
The
di
it is
i minimum
i i
Homozygote individual
183/183
Individu homozygote Individu hétérozygote
189/189
183/189
Courtesy M. Valero
Microsatellite markers to estimate genetic
diversity in L. digitata
Population 1
Low g
genetic diversity
y
Population 2
High
g genetic
g
diversity
y
189
189
187
187
185
185
183
183
Homozygote individual
183/183
189/189
High genetic differentiation between populations (sharing very few genes in common) Courtesy M. Valero
Brown algal genomics
The Ectocarpus genome (200 Mb) project J.-M.
J M Cock
GENOME SEQUENCING : 3,000,000 reads (10X, shotgun)
cDNA SEQUENCING :
100,000 reads (full-length cDNAs)
P. Rouzé / Y. van der Peer
J. M. Cock, Roscoff
- STRAIN SELECTION
- BIOLOGICAL MATERIAL
- LIBRARIES
+ Es Genome Consortium
- LIBRARIES
- SEQUENCING
- ASSEMBLY
- AUTOMATIC ANNOTATION
- EXPERT ANNOTATION
Cock JM et al. (74 authors)
Nature. 2010 Jun 3; 465:617-21
and more than 20 papers during
the two last years.
years.
Brown algal genomics
Large‐scale genome assembly using a genetic map
New Phytologist (2010)
doi: 10.1111/j.1469-8137.2010.03273.x
Red seaweed genomes
The Chondrus
The
Chondrus
genome project
Jonas Collén
é
Catherine Boyen
The Porphyra
The
Porphyra
genome projects
Ulva genome
John h
Bothwell
FSU Jena
The Ulva ggenome p
project
j 150 Mbpp
Towards Genome-Wide Assoc. Survey
Phenotype
Phenotypeanalysis
analysis
Genome-wide methods
make it possible to identify
genes associated with
complex traits, like yield or
disease resistance
Gene
discovery
Genotype analysis
Association analysis
QTL mapping population of Ectocarpus
Gametophytes
(n)
Ec568
Ec32
meiosis
Sporophyte
(2n)
segregating progeny
(…)
( )
(…)
Genotyping / Phenotyping
Gametophytes
( )
(n)
Parthenosporophytes
h t
(n)
Courtesy P. Boudry Ifremer
QTL mapping population of Ectocarpus
Genotyping:
- 400 microsatellites / 60 ind. : already available !
- 40 additional individuals
- SNP markers on the basis of genomes sequences
Phenotyping:
- fitness
fitness-related
related traits: survival to low salinity, growth
- gene expression : eQTL
- other traits of interest… polysaccharides ?
Expected
pec ed ou
outputs:
pu s:
- genetic architecture of observed variation of traits
- comparative mapping of QTLs between sexes,
- comparative mapping of QTLs between ploidy levels
Courtesy P. Boudry Ifremer
Some anticipated outputs
- Large genetic resources for successful
cultivation operations.
-Reliable methods for the genotyping and the
chemical phenotyping
p
yp g of valuable strains
strains..
- Anticipation of the impact of large scale
cultivation of seaweeds on the genetic diversity
of natural populations using genetic markers
- Essential tools for molecular breeding of the
most valuable strains or hybrids.
- Merging population genomics and classical and
quantitative genetics in seaweed aquaculture
-AE
European concerted
t d effort
ff t iis required
i d to
t
increase genetic resources and genomics input!
Thank you
P t
Partnership
hi IDEALG
•
•
•
12 Academics
5 Private companies
1 Technical center
(staff >100)
www.idealg.ueb.eu
Towards GWAS
This approach
Thi
h allows
ll
h
hundreds
d d off genes
with small effects to be identified
In maize, grain yields are correlated
with leaf angle and size. A genomewide association survey (GWAS)
revealed hundreds of singlenucleotide polymorphisms (SNPs)
associated with these traits, providing
invaluable information for breeders.
Reprinted by permission from Macmillan Publishers Ltd. Tian, F., Bradbury, P.J., Brown, P.J., Hung, H., Sun, Q., Flint-Garcia, S., Rocheford, T.R., McMullen, M.D.,
Holland, J.B., and Buckler, E.S. (2011). Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162.
Towards GWAS
GWAS reveals SNPs that
contribute to disease resistance
Similar studies have
led to the
identification of
genes contributing
to other
agronomically
important
p
traits
including drought
tolerance
Reprinted by permission from Macmillan Publishers Ltd Kump, K.L., Bradbury, P.J., Wisser, R.J., Buckler, E.S., Belcher, A.R., Oropeza-Rosas,
M.A., Zwonitzer, J.C., Kresovich, S., McMullen, M.D., Ware, D., Balint-Kurti, P.J., and Holland, J.B. (2011). Genome-wide association study of
quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43: 163-168.